[gmx-users] Umbrella sampling tutorial

[gozde ergin]

Any idea on this topic?

Thanks
> On 07 Oct 2016, at 14:13, gozde ergin <gozdeeergin at gmail.com> wrote:
> 
> Thanks Justin.
> I want infinite dilute bulk that’s why I do not want any surfactant molecule inside the bulk.
> I may put a ‘’wall’’ just below the surface molecules in order to inhibit their travel to bulk but I do not know how to remove this effect from PMF.
> 
> 
>> On 07 Oct 2016, at 13:40, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>> 
>> 
>> On 10/7/16 4:41 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I would like to ask a question about Justin’s tutorial. By using the
>>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>>> effect of this restraint removed during the WHAM?
>>> 
>> 
>> Not to my knowledge, no.  The restraints in the tutorial are there to mimic the fact that there are only five peptides, when in reality, there are millions, so the effects of the forces are quite different in vitro/in vivo.  Restraining one peptide makes the remaining four peptides more stable, more realistic.  WHAM doesn't do anything to change this.
>> 
>>> I want to do a similar thing by applying restraint force on the organic
>>> molecule on the bulk water in order to inhibit their movement inside the
>>> bulk. Should I consider the removing of the restraint in PMF?
>>> 
>> 
>> In the case of freely diffusing molecules, I suspect such a restraint would have a much more profound impact.  Why do you want to do this?
>> 
>> -Justin
>> 
>> -- 
>> ==================================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
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>